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QC Report for Methylation Calling
Input parameters
| value | |
|---|---|
| Sample name | /data/Runs/415630/output/415630-20250125_0254/415630-L3450-Z0010-CACTGCACGAATGAT/415630-L3450-Z0010- CACTGCACGAATGAT.methyl_seq |
| h5 file | /data/Runs/415630/output/415630-20250125_0254/415630-L3450-Z0010-CACTGCACGAATGAT/415630-L3450-Z0010- CACTGCACGAATGAT.methyl_seq.applicationQC.h5 |
Human Genome: Global Methylation Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 72.41 |
| Percent Methylation: std | 11.83 |
| Percent Methylation: median | 74.00 |
| Total CpGs: | 740,717 |
| Coverage: mean | 60.20 |
| Coverage: std | 21.16 |
| Coverage: median | 61.00 |
Human Genome: Details of Per-Read Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: mean | 59.71 |
| Percent Methylation: std | 41.08 |
| Percent Methylation: median | 66.67 |
| Total CpGs: mean | 2.70 |
| Total CpGs: std | 3.01 |
| Total CpGs: median | 2.00 |
Human Genome: Cytosines in Other Contexts Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 73.88% |
| Percent Methylation: Std | 10.13% |
| Percent Methylation: Median | 75.00% |
| Coverage: Mean | 58.64 |
| Coverage: Std | 21.28 |
| Coverage: Median | 60.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.29% |
| Percent Methylation: Std | 13.37% |
| Percent Methylation: Median | 72.00% |
| Coverage: Mean | 32.31 |
| Coverage: Std | 14.34 |
| Coverage: Median | 31.00 |
Human Genome: M-bias plots of mean methylation along reads
M-bias Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.14% |
| Percent Methylation: Std | 9.37% |
| Percent Methylation: Median | 72.44% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 70.54% |
| Percent Methylation: Std | 10.73% |
| Percent Methylation: Median | 73.00% |
Human Genome: M-bias plots of mean methylation on CHH/CHG along reads
M-bias of CHH/CHG Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 67.41% |
| Percent Methylation: Std | 13.78% |
| Percent Methylation: Median | 71.27% |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 71.40% |
| Percent Methylation: Std | 7.58% |
| Percent Methylation: Median | 72.83% |
Control Genomes: Methylation and Coverage Descriptive Statistics
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 1.04% |
| Percent Methylation: Std | 8.14% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 760 |
| Coverage: Mean | 4.30 |
| Coverage: Std | 4.09 |
| Coverage: Median | 2.00 |
| value | |
|---|---|
| metric | |
| Percent Methylation: Mean | 4.04% |
| Percent Methylation: Std | 10.54% |
| Percent Methylation: Median | 0.00% |
| Total CpGs: | 170 |
| Coverage: Mean | 14.53 |
| Coverage: Std | 23.23 |
| Coverage: Median | 5.00 |
Human Genome: Additional Details of CpG Methylation and Coverage
Human Genome: Values of CpG Methylation and Coverage
| value | |
|---|---|
| bin | |
| 10 | 1,976 |
| 20 | 595 |
| 30 | 2,578 |
| 40 | 5,898 |
| 50 | 13,470 |
| 60 | 56,092 |
| 70 | 175,044 |
| 80 | 279,606 |
| 90 | 177,408 |
| 100 | 28,050 |
| value | |
|---|---|
| bin | |
| 10 | 15,902 |
| 20 | 13,073 |
| 30 | 21,983 |
| 40 | 44,073 |
| 50 | 93,688 |
| 60 | 154,926 |
| 70 | 172,430 |
| 80 | 125,723 |
| 90 | 62,806 |
| 100 | 22,570 |
| 110 | 6,443 |
| 120 | 2,132 |
| 130 | 924 |
| 140 | 547 |
| 150 | 414 |
| 160 | 326 |
| 170 | 257 |
| 180 | 186 |
| 190 | 191 |
| 200 | 2,123 |
| value | |
|---|---|
| bin | |
| 10 | 2.15% |
| 20 | 3.91% |
| 30 | 6.88% |
| 40 | 12.83% |
| 50 | 25.48% |
| 60 | 46.39% |
| 70 | 69.67% |
| 80 | 86.65% |
| 90 | 95.12% |
| 100 | 98.17% |
| 110 | 99.04% |
| 120 | 99.33% |
| 130 | 99.45% |
| 140 | 99.53% |
| 150 | 99.58% |
| 160 | 99.63% |
| 170 | 99.66% |
| 180 | 99.69% |
| 190 | 99.71% |
| 200 | 100.00% |